- g.setColor(Color.red);\r
- g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
+ int startSeq = av.startSeq;\r
+ int endSeq = av.endSeq;\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ startSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
+\r
+ endSeq =\r
+ av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
+\r
+ }\r
+\r
+\r
+ scalew = (float) width / (float) fullsizeWidth;\r
+ scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
+\r
+ boxX = (int) (startRes * av.getCharWidth() * scalew);\r
+ boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
+\r
+\r
+\r
+ if(av.hasHiddenColumns)\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+ else\r
+ boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);\r
+\r
+\r
+ boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);\r
+\r
+\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ if (miniMe != null && !resizing)\r
+ {\r
+ g.drawImage(miniMe, 0, 0, this);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Verdana", Font.BOLD, 15));\r
+ g.drawString("Recalculating", 5, sequencesHeight / 2);\r
+ g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20);\r
+ }\r
+\r
+\r
+ g.setColor(Color.red);\r
+ g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
+ g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
+\r